Package: treeplyr 0.1.11

Josef Uyeda

treeplyr: 'dplyr' Functionality for Matched Tree and Data Objects

Matches phylogenetic trees and trait data, and allows simultaneous manipulation of the tree and data using 'dplyr'.

Authors:Josef Uyeda [cre], Luke Harmon [aut]

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treeplyr.pdf |treeplyr.html✨
treeplyr/json (API)

# Install 'treeplyr' in R:
install.packages('treeplyr', repos = c('https://phylotastic.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/uyedaj/treeplyr/issues

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:

On CRAN:

14 exports 33 stars 2.50 score 61 dependencies 97 scripts 144 downloads

Last updated 2 years agofrom:90e6412e9d. Checks:OK: 1 WARNING: 8. Indexed: no.

TargetResultDate
Doc / VignettesOKSep 06 2024
R-4.5-win-x86_64WARNINGSep 06 2024
R-4.5-linux-x86_64WARNINGSep 06 2024
R-4.4-win-x86_64WARNINGSep 06 2024
R-4.4-mac-x86_64WARNINGSep 06 2024
R-4.4-mac-aarch64WARNINGSep 06 2024
R-4.3-win-x86_64WARNINGSep 06 2024
R-4.3-mac-x86_64WARNINGSep 06 2024
R-4.3-mac-aarch64WARNINGSep 06 2024

Exports:detectAllCharactersdetectCharacterTypefilterMatrixforceFactorforceNamesforceNumericgetVectorhasNamesmake.treedatapaint_cladesreordertdapplytreedplytreeply

Dependencies:apecliclusterGenerationcodacodetoolscolorspacecombinatcpp11DEoptimdeSolvedigestdoParalleldplyrexpmfansifarverfastmatchforeachgeigergenericsggplot2ggseqlogogluegtableigraphisobanditeratorslabelinglatticelazyevallifecyclemagrittrmapsMASSMatrixmgcvmnormtmunsellmvtnormncbitnlmenumDerivoptimParallelphangornphytoolspillarpkgconfigquadprogR6RColorBrewerRcpprlangscalesscatterplot3dsubplextibbletidyselectutf8vctrsviridisLitewithr

Readme and manuals

Help Manual

Help pageTopics
Anole dataanolis
Apply detectCharacterType over an entire matrixdetectAllCharacters
Function to detect whether a character is continuous or discretedetectCharacterType
Function for filtering rows from an object of class 'treedata'filter.grouped_treedata filter.treedata
Filter a matrix, returning either all continuous or all discrete charactersfilterMatrix
Function for checking whether a treedata object contains only factors and for forcing data columns into factor formatforceFactor
Force names for rows, columns, or bothforceNames
Function for checking whether a treedata object contains only numeric columns and for forcing data columns into numeric formatforceNumeric
A function for returning a named vector from a data frame or matrix with row namesgetVector
Function for grouping an object of class 'treedata'group_by.treedata ungroup.grouped_treedata
Row and column name checkhasNames
Function for making an object of class 'treedata'make.treedata
Function for mutating an object of class 'treedata'mutate.grouped_treedata mutate.treedata
Add regimes to a treedata objectpaint_clades
Reorder a 'treedata' objectreorder reorder.treedata
Function for selecting columns from an object of class 'treedata'select.grouped_treedata select.treedata
Choose rows by their ordinal position in the tbl for an object of class 'treedata'slice.treedata
Function for summarizing an object of class 'treedata'summarise.grouped_treedata summarise.treedata summarize.grouped_treedata summarize.treedata
Apply a function over all treedata object columns and return a list of results, analogously to the normal apply functiontdapply
Run a function on a 'treedata' objecttreedply treedply.treedata
Run a function on the phylogeny of a 'treedata' objecttreeply treeply.treedata
treeplyr: 'dplyr' Functionality for Matched Tree and Data Objectstreeplyr
Defunct functions in treeplyrtreeplyr-defunct